In a four-page memo last October to Public Safety Minister Steven Blaney, Canada Border Services Agency president Luc Portelance said he was "unable to recommend that we consider a third season at this time."
The memo, obtained by The Canadian Press under the Access to Information Act, noted the program had raised the ire of civil libertarians and faced a formal privacy complaint.
It concluded the "'risk/reward ratio' for the project is questionable."
However, the border agency said the minister gave the nod in January to federal participation in a new season of the show. Filming is now underway in British Columbia and Ontario.
Border Security: Canada's Front Line, which began airing on the National Geographic Channel in 2012, chronicles encounters between border officers and the public. The unscripted series has been seen by more than 11 million Canadians and airs in over 50 other countries.
The border agency contributes $200,000 in communications support to the show annually along with some management oversight.
In the Oct. 9 memo to Blaney, Portelance said the program represented "good value for money" and an innovative way to inform Canadians about the agency's work.
"Notwithstanding the popularity of the show, there continues to be some risk in participating in a project of this type," Portelance added in the memo, which was prompted by an inquiry about a new season from the private production company behind the series.
Filming of the border agency's arrest of allegedly undocumented workers last year led to a public outcry about the appropriateness of the government's participation in the show.
The groups No One is Illegal called for the program's cancellation and the British Columbia Civil Liberties Association voiced its objections. The federal privacy commissioner is investigating a complaint about the show.
In addition, Portelance wrote, the TV program "is not directly linked to either our key priorities or our core business."
"While we believe that the show engenders pride among CBSA employees, and perhaps Canadians in general, there are no measurable outcomes that can be readily attributed to this show."
Given this, and the "various challenges" the project had faced, he recommended that Blaney "not approve" participation in a third season.
Blaney spokesman Jason Tamming confirmed to The Canadian Press that the minister gave a new season the green light, but he did not provide any details.
The border services agency changed its position on continuing with the show, though it is not clear exactly why.
The border agency committed to a third season "after thorough internal discussions, and with the support of the Minister of Public Safety and Emergency Preparedness," agency spokesman Luc Nadon said in an emailed statement.
The agency refused to say who initiated a reopening of the file following the October 2013 recommendation not to proceed, or whether the minister was involved in the internal discussions. It would say only that the minister provided final approval on Jan. 21.